[ensembl-dev] Core API quits with no error messages

[Damian]

Hi Ian.
Thanks for the quick reply.

I'm using Ensembl Human Core 62_37g.

We have to stick to this version because all our previous work was done 
with it.

Your code changes do indeed work but only with the 63 release.
Is there a way to identify these problem cases in 62 and to skip them?

if(defined($gene)) doesn't work for me since the gene object is indeed 
returned.

Damian



On 08/26/2011 10:16 AM, ian Longden wrote:
> What version of the API are you using?
> ENSG00000256461 has been archived and is not in release 63 so that
> could be part of it.
>
> also add -verbose =>  1 to the load_registry_form_db to see which
> databases it is connecting to.
>
> So i modified your script to use our server as a test
> #######################################################
> use Bio::EnsEMBL::Registry;
>
> my $reg = 'Bio::EnsEMBL::Registry';
>
> $reg->load_registry_from_db(
>         -host =>  'ensembldb.ensembl.org',
>         -user =>  'anonymous',
>         -db_version =>  63,
>         -verbose =>  1
> );
>
>
> my $GA = $reg->get_adaptor('Human', 'Core', 'Gene');
>
> my $gene = $GA->fetch_by_stable_id('ENSG00000256461');
>
> if(defined($gene)){
>
>    my @exons = @{ $gene->get_all_Exons() };
>
>    foreach my $e (@exons) {
>      print ">" . $e->stable_id() . "\n";
>      print $e->seq->seq . "\n\n";
>    }
> }
> else{
>    print "Gene could not be found\n";
> }
>
> exit;
> ##################################################################
> which gave me the list of databases and also the message:-
> Gene could not be found
>
> -Ian Longden
> EnsEMBL Developer.
>
>
> On Fri, Aug 26, 2011 at 2:36 PM, Damian<dfermin at umich.edu>  wrote:
>> Hello.
>>
>>
>> I don't know how to debug this problem with the Core API in perl.
>>
>> Here is the code:
>> ####################################################
>> use Bio::EnsEMBL::Registry;
>>
>> my $reg = 'Bio::EnsEMBL::Registry';
>> $reg->load_registry_from_db(
>>         -host =>  '127.0.0.1',
>>         -user =>  'nesviLab'
>> );
>>
>>
>> my $GA = $reg->get_adaptor('Human', 'Core', 'Gene');
>>
>> my $gene = $GA->fetch_by_stable_id('ENSG00000256461');
>>
>> my @exons = @{ $gene->get_all_Exons() };
>>
>> foreach my $e (@exons) {
>>     print ">" . $e->stable_id() . "\n";
>>     print $e->seq->seq . "\n\n";
>> }
>>
>> exit;
>>
>> ####################################################
>>
>>
>> When I run this code, the output is the first exon of the array and that's
>> it:
>>> ENSE00002226834
>> The sequence of the exon is never written out.
>> The script does not throw an error and the program does exit.
>> Running 'top' on my computer shows that the script is not even using up CPU
>> cycles.
>>
>> This only happens with genes on chromosome 1. The above code runs to
>> completion with any genes from chromosomes 2..Y
>> Any idea what's going on? Any and all help is greatly appreciated.
>>
>> I'm running the Ensembl Core version 62 on RHEL 5.4 (64bit).
>> Perl version: 5.8.8
>> MySQL version: 5.0.77
>>
>> Damian
>>
>> --
>> ------------------------------------------------------------------------------
>> Damian Fermin, Ph.D.
>> Pathology Department
>> University of Michigan
>> 4237 Medical Science I
>> 1301 Catherine
>> Ann Arbor, MI 48109-0602
>> 734.615.0302
>>
>> "There is No Gene for the Human Spirit"
>>         -- GATTACA
>> ------------------------------------------------------------------------------
>>
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
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>>
>

-- 
------------------------------------------------------------------------------
Damian Fermin, Ph.D.
Pathology Department
University of Michigan
4237 Medical Science I
1301 Catherine
Ann Arbor, MI 48109-0602
734.615.0302

"There is No Gene for the Human Spirit"
	-- GATTACA
------------------------------------------------------------------------------